In Darkest Days
by D.P.Balding
Summary: Captain Janeway has to assemble her old crew and take back Voyager in order to save the Federation from it's darkest enemy...Starfleet! Multiple romances. Please do leave reviews as this is my first story on here. Thank you.
1. Prologue

"Do you have any idea how ridiculous you look right now?" Tom Paris asked, as he looked at his friend, Harry Kim. Harry rolled his eyes as he shook his head, looking at his white Starfleet Dress uniform. Tom, who was going to the same place as Harry, was wearing his new Starfleet uniform.

"Nice Tom, real nice. You know how to cheer me up, don't you?" Harry asked. Tom grinned and placed a hand on Harry's shoulder.

"Harry, Harry, Harry. It's not my job to cheer you up, it's my job to be honest with you." Tom said. As the two of them walked out of Harry's house, they looked up at the moon.

"I still can't believe we're here." Harry said.

"What, back on Earth?" Tom asked, looking at Harry, who nodded. "Trust me, you're not the only one. I was speaking with Chakotay yesterday, everyone has been going to him for advice. I know all the Maquis were pardoned, but still, they find it hard being in demand for Starfleet."

"How's B'lanna handling it?" Harry asked, as the two of them walked down the street.

"She's a rock, as usual. She's being wooed by Starfleet Corps of Engineers, by Starfleet Command and even a number of ships. She's still working on Voyager for now, although, and you never heard this from me, the admiralty are thinking of decommissioning her." Tom explained. Harry knew he had heard that from his father, and shook his head.

"Tom, you know that Captain Janeway won't let that happen." Harry said.

"I hope not. I intend to fly that ship again." Tom said.

"I thought you were being assigned to be a test pilot for Starfleet's newest ships?" Harry asked, frowning.

"They asked, I said no." Tom replied. Harry looked shocked, causing Tom to chuckle at the sight of it. "Harry, I can't go risking my life on a test ship, not now I have a wife and baby to content with. Miral may be six months old, but she's quite a handful." Tom said. Harry smiled, and looked down at the ground.

"I envy you, Tom." Harry said. "I tried to get back with Libby, but she's married now."

"But you knew that." Tom said, frowning. He then let out a loud laugh. "Harry, you never change. A hologram, a Borg, the wrong twin, a dead ensign, an alien whose people shunned outside contact and now a married woman. Do me a favour and never change." Tom said.

"I won't, don't worry." Harry said, as they walked down another street. As they did, they stopped, seeing a group of people standing just ahead of them, staring at them both, all wearing black outfits and balaclava's, covering their faces.

"What do you think they want?" Tom asked.

"They don't look friendly, do they?" Harry asked. He turned and saw more people behind them, surrounding them.

"Okay, get ready to run, I'll distract them." Tom said.

"I'm not leaving you Tom." Harry said.

"You won't need to." A female voice said, from behind them. They turned, and saw Kathryn Janeway.

"Captain? What's going on?" Harry asked, as the group approached them.

"I'm recruiting you both for an important mission." Kathryn said, as the group lifted their masks. The nearest one to Kathryn was Chakotay, with Seven of Nine and The Doctor standing next to them.

"What's going on?" Tom asked.

"I'll explain in a minute." Kathryn said, nodding at several of the group. They produced transporter enhancers, and placed them around the group. Confused, Tom and Harry looked at one another, but stayed still, especially since they knew that Janeway and Chakotay wouldn't be doing this unless there was a damned good reason. Small devices were placed on the transporter enhancers, and Tom knew they were isolinear tags. As the usual feeling of being transported swept over them, Tom found himself smiling as he found himself in a Cargo Bay on Voyager. The crew removed their masks, and they looked at each other, heading out of the cargo bay, and soon, Tom, Harry, Seven, Chakotay, Kathryn, Tuvok and The Doctor was left.

"Okay, does someone want to tell me what's going on?" Tom asked, looking at them.

"We're stealing Voyager, and going on the run." The Doctor said, with a serious look.

"Okay, this is a joke, right?" Harry asked, looking at them to see if there was a hint of humour.

"Sorry Harry, no joke." Chakotay said, looking at the man.

"Seven and Chakotay have been doing some research, and we've discovered something unsettling, so I've assembled the old crew, and decided we need to do something drastic. We're stealing Voyager so we can save the Federation." Kathryn said, leading them all out of the Cargo Bay, just as B'lanna raced over to them.

"The warp core is ready to go, we've got transphasic torpedoes ready and our armour systems are prepared." B'lanna said.

"B'lanna? Where's Miral?" Tom asked, concerned.

"Your father is in our quarters looking after her with your mother." B'lanna said, almost dismissively.

"B'lanna, what's going on?" Tom asked.

"Tom, I'll tell you everything later." B'lanna said, smiling at him.

"B'lanna, go with him and tell him, I'll explain everything to Harry." Kathryn said. B'lanna nodded, and Tom went with B'lanna.

"Captain, what's going on?" Harry asked, as she led him out.

"We're facing the most dangerous enemy that we've ever faced." Chakotay said.

"WHO!" Harry exclaimed, feeling more frustrated. Kathryn sighed.

"I'm sorry to tell you, but we're going up against...Starfleet!"


	2. Chapter 1 - The Escape

Chakotay looked at Harry, and felt sorry for the man. He remembered when he had first learnt of the threat that was facing the Federation, when Seven had told him, and he had been just as shocked. He had spent years fighting the Cardassians, and the Federation to a degree, but he had always believed in their true ideals, which was why he had agreed to be Kathryn's first officer in the Delta Quadrant, but he had never wanted to believe that Starfleet could be such a dangerous enemy. "Harry, I know what we're telling you is hard to believe, but we wouldn't lie to you." Chakotay said.

"Neither would we have pursued such a course of action if we did not have evidentiary proof, Ensign Kim." Seven said.

"I...I...I know." Harry said, finally being able to speak. "Captain, what are we doing?" He asked. Kathryn put a reassuring arm around his shoulder, and looked at him as she had often done as they walked through the corridor of the ship.

"To be honest Harry, I don't know. Right now, we're getting away as quickly as we can, before we're discovered. We've managed to convince Admiral Paris and he helped us to get the codes we need to get aboard Voyager. The easy part will be to get away from Earth. The hardest part will be to return." Kathryn said.

"Captain...after everything we've been through, I'll help in any way I can, but...surely not everyone in Starfleet can be involved?" Harry asked, desperately hoping for some glimmer of light.

"No, not everyone, but at this point, we're not sure who we can trust. There is a method to detect who can be trusted, but it requires their consent." Kathryn said.

"Or for us to kidnap them and run a sub-molecular scan on them." The Doctor added.

"Which we can't really do without being noticed. I spoke with the Doctor, and Seven, and from there we made a plan." Chakotay said, as they reached the nearest turbolift. "We don't know how deep it goes, but we're positive that Starfleet Command is in on this. We spoke with Tom's father, and explained everything after testing him. Luckily he trust's Kathryn more than anyone." He added, as they took the turbolift up towards the bridge.

"I guess." Harry said. He sighed. "That promotion is out of the window."

"Promotion?" Kathryn asked.

"I was on my way to a party for some of the best in Starfleet. I was told that if I played it right, I would be a full Lieutenant by the end of the evening." Harry explained. "Tom was coming with me." He added. Chakotay and Kathryn looked at one another, nervously.

"Looks like we got to them just in time." Chakotay said.

"Sorry Harry, you probably would have been converted tonight, for lack of a better word. I was told a similar thing the other night." Chakotay said. "I was to be offered my own ship."

"And I was going to get Voyager back. We managed to delay the party, but we were due to be there tonight as well, hence the rush." Kathryn said.

"So how do you know that Tom and I are ourselves?" Harry asked, as they reached the bridge.

"We scanned you during transport." Kathryn replied, looking around the darkened bridge. She smiled, and made her way to the centre seat, just as Tom arrived on the bridge.

"Captain, B'lanna said we should have warp capability right away." Tom said, taking his place at the helm.

"Wait a moment...how do I know you're not the ones who are conspiring against Starfleet?" Harry asked, as a cold shiver ran down his back. Chakotay smiled at Harry, and nodded.

"That's why I know you're still you. You're still cautious and careful." Chakotay said. Harry nodded.

"Still a valid question." Harry said. Kathryn nodded.

"It is. Well, I can show you scans but they would mean nothing." Kathryn said. She stood in front of Harry, and looked into his eyes. "Once again, I need to ask you for your trust. You know me as well as anyone else here. I want you to look into my eyes, and tell me if I'm not me." Kathryn said firmly. He looked into her eyes, and as he saw the same person he had seen so many times before, the nervous feeling he got disappeared. Kathryn could tell, smiled and embraced Harry in a hug. "It's really good to see you again Harry." Kathryn said, patting his back before breaking apart.

"Not as good as it is to see you too, Captain." Harry said. She smiled, and Harry made his way to his station.

"Are we ready to go?" Kathryn asked. Chakotay sat down and checked his console.

"We're ready Kathryn." Chakotay said. Kathryn nodded, and looked on as several crewmembers came onto the bridge, taking their station, followed by Admiral Owen Paris.

"Kathryn, I've got the codes you will need." Owen said.

"Harry will need them." Kathryn said, entering something into her console. Owen walked over to Harry and handed him a PADD. Harry accepted it, looked at the PADD and began to enter in the codes.

"Captain, I have control of Spacedock doors, and we're ready to go." Harry said.

"Shields and weapons at your discretion Captain." Tuvok added. B'lanna's voice filtered through the comm. system.

"_Engineering to bridge, we're ready to power up._" B'lanna said. Kathryn nodded, and closed her eyes. She thought for a moment of everyone she was leaving behind, reminding herself why she was doing this. She looked at Chakotay, who nodded. He took her hand and squeezed it softly, which comforted her.

"B'lanna, light us up." Kathryn ordered. The lights on the bridge came on, and all around the ship, every light came on, sickbay and the mess hall powered up, and every room showed signs of life. The warp core began to pulsate with life again, and on the outside of the ship, the running lights came on, showing the logo's of Starfleet, and finally showing Voyager's name.

"Disengage us from dock controls." Chakotay ordered. Harry entered the codes he had been given.

"We're clear, Commander." Harry said.

"Shields are up. I have also activated transport inhibitors throughout the ship, as a secondary precaution." Tuvok reported.

"Tom, take us out." Kathryn ordered. "One quarter impulse power."

"One quarter impulse, aye Captain." Tom replied, as Owen sat next to Kathryn.

"You know impulse isn't allowed in spacedock, don't you Kathryn?" Owen asked.

"What we're doing isn't allowed." She reminded him, with a small smile.

"Good point." He agreed. Voyager lurched forward towards the massive set of space doors, which began to open.

"We're receiving a hail from Starfleet Command, ordering us to stand down." Harry reported.

"Ignore it." Kathryn said, although she knew Harry already had.

"Looks like the Adelphi, the Melbourne and the Odyssey are being ordered to power up." Harry said.

"Ensign Kim, transmit the second command code I gave you to the location shown." Owen ordered. Harry nodded, and as soon as the code was transmitted, the lights around spacedock began to flicker.

"What was that?" Tom asked.

"I had B'lanna prepare a little present to help us. We just scrambled all computer systems for at least ten minutes." Kathryn said.

"Using Spacedock's own computer to transmit it." Harry added, looking at his console, impressed, as Voyager began to fly through the doors.

"Tom, as soon as we're clear, set a course for the Karandis system, maximum warp." Kathryn ordered.

"Won't they track our warp trail?" Harry asked.

"I created a virus to eliminate our warp trail from Starfleet's computer." Seven said.

"And B'lanna is using a new program to mask our warp trail, whilst creating several false ones." Chakotay replied, as Voyager moved away from Spacedock.

"Just checking." Harry said, smiling, as he felt warmth run through his body. After all, despite the situation, he was home again.

"We're clear of Spacedock." Tom said.

"Then by all means Tom, engage." Kathryn ordered. Voyager moved away from Spacedock, and in a flash, she disappeared at Warp, leaving Earth behind.

_Again, all reviews are welcome. I know I only posted the prologue tonight, but my first review made me want to write the next chapter right away, so I did. Hope you all enjoy it :)_


	3. Chapter 2 - Dark Days

*Chirp Chirp*

"Captain on the bridge." Commander Tuvok's voice said as Reg stepped off of the bridge and onto Voyager's bridge. He smiled at Tuvok.

"Thank you Tuvok." He said, before going towards the centre seat.

*Chirp Chirp*

"Captain Barclay, we're ready to leave." Harry said from Ops. Reg smiled.

"Very good Harry." Reg said, as he sat down. He smiled and looked at the helm, where Tom Paris sat. Next to him was Deanna Troi, who smiled at him.

"Reg, are you nervous?" She asked softly.

"Not with you by my side Deanna." Reg replied confidently. She smiled, leant in and kissed him gently on the lips.

*Chirp Chirp*

~Where is that chirping coming from?~ Reg asked himself. Then he realised that it was the chime to his apartment.

Opening his eyes, Reg smiled as he saw Neelix asleep next to him on the bed. Reg yawned as his comm. badge went off. He tapped it, frowning. "Barclay here." He said.

"_Reg, it's Pete. I need you to open your front door._" Commander Pete Harkins' voice filtered through his comm. badge.

"I'm on my way." Reg said, quickly pulling on his dressing gown. He walked quickly to the front door, and saw Pete, along with two armed security guards and another officer that Reg didn't recognise. "Pete, w...w...what's going on?" He asked.

"I'm sorry to wake you Reg, but this is Lt. Commander Davis from Starfleet Security. He needs to talk to you." Pete said, as Reg allowed them into his apartment.

"W...w...w...what about?" Reg asked.

"Commander Barclay, earlier this evening, Captain Kathryn Janeway, along with her crew, stole the USS Voyager out of Spacedock. You seem to have become friendly with the crew, did any of them communicate with you about their intentions?" Davis asked.

"N...n...no, why would they?" Reg asked, confused about what was going on.

"Because they trust you. They would have tried warning you, perhaps. When was the last time you saw anyone on the crew of Voyager?" Davis asked, tapping something into a PADD.

"Umm...I saw Harry and Tom yesterday." Reg replied. "W...w...we were talking about Harry's possible upcoming promotion."

"Are you sure about that?" Davis asked.

"That's enough, Lt. Commander Davis." Pete said, putting emphasis on the rank. "Reg already said that he wasn't contacted and that's good enough for me."

"With all due respect, Commander, we don't know if it is good enough for us. Commander Barclay has had extensive contact with all of the fugitives, including Admiral Paris." Davis said.

"Ad...ad...admiral Paris did this as well?" Reg asked, shocked. He had never known the man to do anything against regulations, which suddenly made him start to think.

"See? Now that is genuine surprise." Pete said. He looked at Reg. "Get some rest Reg, we'll be needing your help in the morning at the lab."

"I...I...I'll be there." Reg said, nodding. Pete ushered the security officers out, but stayed with Reg. For his part, Reg was still dumfounded. He still couldn't believe what he had heard, and he needed to think quickly. Why would they have done this? He went to his computer, and sat down, but stopped as he saw something flashing on the screen.

"What's that Reg?" Pete asked.

"I...I don't know. It wasn't there when I went to bed." Reg said. Pete nodded, as Reg sat down. Turning on the screen, he saw a message waiting for him, the face of Kathryn Janeway.

"_Hello Reg. Soon people will be coming for you, and I'm the cause of that. I couldn't risk talking to you in person because you were always surrounded by Starfleet officers, but after everything you've done for us, I couldn't leave you alone in the dark. I believe Starfleet is compromised from within, and we're all in danger. I'm taking Voyager somewhere safe, I can't tell you where, but you need to leave, now. Get anyone you trust completely, and get away from Earth, now._" Kathryn said. Reg and Pete exchanged looks, frowning.

"W...w...what do you think she means?" Reg asked.

"I don't know, but I've had a bad feeling for a while now." Pete said. "Especially with the Admiral leaving."

"So...w...w...w...what now?" Reg looked at the screen again, which was frozen.

"Now? We need to get out of here, but we need transport." Pete said. Reg smiled, and tapped something into his computer.

"L...l...luckily, I have a few friends in town." Reg said.

"Please tell me they're actual friends?" Pete said, concerned. Pete nodded as the screen changed to show Captain Jean Luc Picard on the bridge of the Enterprise.

"_Mr. Barclay, how the heck are you?_" Picard said, smiling at him.

"I...I...I've been better, Captain." Reg said. Pete looked at the screen.

"Captain Picard, I'm Commander Harkins, Reg's superior officer. We need your help." Pete said.

"_Well, we are about to leave on the trail of Voyager, so this isn't really a good time._" Picard said.

"It's about that. We were left a message by Captain Janeway saying that Starfleet could be compromised, and we could be targeted next. Can you beam us up and take us with you?" Pete asked.

"_Did she leave any details?_" Picard asked, frowning.

"N...n...no, Captain, just that I needed to leave." Reg said. Picard nodded, and turned to someone on the screen.

"_Prepare for transport._" Picard said. Reg stood up, and picked up Neelix who was purring at his feet. Reg turned around as he heard a crash and saw the door to his apartment smash open, just as a number of people wearing dark outfits burst in. As they fired at Reg and Pete, the transporter washed over them, and the phaser shots passed through where they had been harmlessly.

Standing on the bridge of the Enterprise, Reg was shaking heavily, with Pete trying to hold him steady. "Looks like Captain Janeway was right." Picard said, as the screen changed to show Earth.

"It won't be long before the Enterprise is targeted. Do you have your entire crew aboard or are any of them on shore leave?" Pete asked.

"We were preparing for departure, so we're ready." Picard said, as Deanna Troi stood up.

"Reg, I'll take you and Commander Harkins to guest quarters." Deanna said, smiling.

"Thank you Counselor." Picard said. "Mr. Data, get us out of here."

"I suggest we go to Qo'nos, Jean Luc. Worf and Chancellor Martok will need warning." Will Riker said. Picard nodded.

"Agreed." He replied. "Mr. Data, make it so." He ordered.

"Captain, the USS Drake is targeting weapons!" Lt. Commander Daniels told him.

"Raise shields! Red alert!" Riker ordered. Two seconds later, the ship shook from weapons impact, just as the Enterprise moved away from Earth, quickly, with the Sovereign Class USS Drake following.

"Return fire, target their weapons and propulsion only, Phasers and Photons only" Picard ordered, feeling a darkness sweep over him as he gave the order to fire on another Starfleet vessel, something he had hoped he would never need to do. Phaser beams fired from the Enterprise, followed by a number of photon torpedoes, all of them striking the shields of the USS Drake.

"T...t...this is...is this...happening?" Reg asked.

"Come on Reg." Deanna said, leading him off the bridge, whilst Pete remained, and took a seat on the guest seat as the Enterprise shook again.

"Jean Luc, we need to use Quantum torpedoes." Will said.

"That's a Starfleet ship." Picard said.

"And we have very limited options." Will reminded him. Picard nodded, and looked at Daniel.

"Firing Quantum torpedoes." He said. The blue torpedoes sped away and impacted on the Drake, causing more damage and piercing their shields, and as they did, an explosion could be seen on the hull of the Drake, causing the ship to stop moving. The Enterprise, however, didn't stop and sped to warp, leaving Earth and the Drake behind.

_Wow, I never realized how many people would like my story. Well, I hope you all enjoy this chapter, and keep the reviews coming, you keep pushing me to write more and more, so the more reviews I get, the quicker I write :) Thank you for the comments, I love them. More to come soon :)_


	4. Chapter 3 - Heartache to Heartache

As Voyager flew through space at high warp, the entire crew was on edge, and as he walked through the corridors, Chakotay knew he couldn't blame them. He was feeling on edge himself, more so than any of the times they had been in the delta quadrant...well, except for when they were fighting The Borg. As his mind ran along that train of thought, he wondered how Unimatrix Zero was doing, especially since they had destroyed the Transwarp Hub and the Borg's Transwarp network. He knew it would be a while before they heard from the Borg again, but in the next encounter, they would have a much better chance, especially with the Transphasic Torpedoes. He stopped thinking of the Borg since there was only one drone, or rather former drone, he wanted...no, needed to see. Chakotay also knew where she would be, and as he walked into Astrometrics, his guess was right: Seven was at her usual station, with Icheb helping her. He saw them both working hard, and smiled. "Seven, what do you have so far?" He asked.

"I have been working with Icheb to attempt to hack into Starfleet's primary databases, but so far we are not succeeding. However, I believe that we are now on Starfleet's most wanted list." Seven replied.

"We knew that was a possibility. Any ships nearby?" He asked.

"The USS Philadelphia is the closest ship, twelve light years away. There is also the USS Phoenix, the USS Prometheus and the USS Apollo within range. However, none of those ships have detected us, or if they have, they are ignoring us. It would appear that Lt. Torres' modifications are working." Seven said, moving from one console to the next.

"I have scanned the Karandis system, and there is no activity near it. We can hide there for a time, and the planet's rings will shield us from any sensors." Icheb added.

"Very good." Chakotay said. He then looked at Icheb. "Icheb, can you give us a few minutes please?"

"Of course, Commander." Icheb agreed, nodding as he left Astrometrics. Chakotay looked at Seven.

"How have you been?" He asked gently.

"Fine, Commander. I am fully maintained and I have no problems regenerating." Seven said.

"That's not what I meant, and you know it Seven." Chakotay said, as he took her hand in his. She looked at the hand and then at him.

"I know." She admitted. "But this...Chakotay, this...we won't work." Seven said.

"I thought you loved me, Seven. That's what you told me." Chakotay said. Seven looked at him, and then looked down.

"I...thought I did. But I do not know what love is. However, I know that what I feel for you is affection...but I do not believe it to be love. Neither do I believe that you love me, at least not fully." Seven said. Chakotay looked dumbstruck.

"Seven, you don't know how I think, how I feel." Chakotay told her.

"But I do. I know exactly how you think and feel, and it is not love you feel. If it was love, you would have come with me four months ago." Seven said.

"I couldn't. I had too much to do, and you know it." Chakotay told her, as he turned and leant on a console for support.

"I know. But deep down, you knew you wouldn't have come with me. You couldn't give everything up, and it was unfair for me to ask you to do so." Seven explained. She held his hand and looked into his eyes. "You taught me so much about love...and about humanity...and I will always love you for that. But you and I both know where your heart lies." Seven said. Chakotay looked down, unable to look at Seven, knowing who she meant, and what was worse, knowing she was right.

"Seven, I..." He started, but Seven but a finger to his lips.

"You do not need to say it." She said softly. She smiled at him. "I know. You know. But she does not. You need to tell her, sooner rather than later. Just...promise me you will tell her." Seven said. Chakotay nodded.

"I promise." He replied. Seven embraced him in a hug, and then pulled back.

"Now go. I will be okay." Seven said. Chakotay nodded, turned and walked for the exit. As he left Astrometrics, he saw Icheb moving to head back in, so he shook his head.

"She needs to be alone right now." Chakotay said. Icheb frowned and looked at him.

"What has happened? Have you terminated your romantic liason with her?" Icheb asked. Chakotay flashed the young man a soft smile.

"We usually call it breaking up, but yes. Go and rest. Seven will call you when she needs you." Chakotay said. Icheb didn't argue with the man. Instead, he turned and left. Chakotay looked back at the doors, and walked away.

Seven watched the doors close, and then allowed herself to sink to the deck, leaning against the console for support, tears streaming down her eyes. She could hardly believe what had happened, and even though she had known it was coming, it had struck her hard. She felt more pain than she had anticipated, and now she felt alone. As she sat there, crying, she didn't hear the doors open, neither did she see a figure standing near to her, at least not right away. The figure ran to Seven, and wrapped her arms around her tightly. "Seven, what's wrong?" Naomi Wildman asked, looking sad as well, sad to see her friend upset.

"I...I do not believe you would understand." Seven said. Naomi shook her head.

"Try me." She said. Seven shook her head.

"It would be...inappropriate for me to do so." Seven told her. Naomi sighed.

"Did you and Chakotay have a fight?" Naomi asked.

"No...I told him that our relationship would not work because his heart belongs to another, and I released him from his romantic involvement with me." Seven explained.

"That's the worst way to explain a break up I've ever heard." Naomi said softly. "I'm sorry, Seven." She said. She went to the replicator, and replicated a box of tissues. "Here. Whenever mom's upset, she always uses this."

"Thank you, Naomi Wildman." Seven said, accepting the tissues and wiping her tears.

"I know it hurts, but if you ever want to talk, I'm here." Naomi said. Seven nodded as the two women stood up.

"Thank you." Seven said. "What brought you down here?"

"I needed to see you. I did as you asked, I scanned the ship with your scanner, and nothing showed up." Naomi said. Seven nodded.

"That means we are who we are meant to be. Thank you." Seven said, as she started to work at a console. "Naomi, do you miss your father?" Seven asked. Naomi was a little startled by the question, it was the first time Seven had asked such a question.

"Sure, I guess. I mean, I've only met him a couple of times, so I don't feel that close to him yet." Naomi replied.

"I know how that feels. I still feel like I do not know my parents, even though I have spoken with Irene Hansen, my father's sister. She has tried to make me a part of the family, but I never felt like I belonged with them." Seven said.

"I feel the same way. Voyager is my home, not Earth or K'taria." Naomi agreed. "I think the crew feel the same way."

"More than likely. Ever since I...had my implant removed, I have been more open to emotions, and sometimes they have overwhelmed me, with feelings of loneliness, and I find that feeling gone now." Seven explained.

"That's because you're home now Seven." Naomi replied, with a small grin.

"Yes...and now we must protect our home." Seven said.

"We will. Captain Janeway doesn't know how to fail, does she?" Naomi asked. Seven looked at the girl and then at the large screen for a long time, remaining silent for a few moments, before speaking.

"No...no she does not."

_Wow, I can't believe how quickly this is coming out. I even felt myself crying with Seven. Did any of you? Did I handle this well? Do you know who 'she' is? Please leave me more reviews, I love your reviews. This chapter is for ByaSouthernLady, who wished for me to update quickly, and who was the first to follow my story. I hope you enjoy reading this as much as I enjoyed writing it._


	5. Chapter 4 - Explanations

As Tom walked into his and B'lanna's quarters, he smiled as he saw Miral crawling around on the floor. As soon as Miral saw him, her eyes lit up. "Dada!" She said, crawling towards him. Tom bent down and scooped her up, and as he did, she flung her arms around him, or tried to, and pulled herself closer to him.

"Hey sweetie." He said, kissing his daughter. He smiled at his mother, who began to tidy up Miral's toy's. However, as she saw that happen, Miral began to struggle to get down to the ground.

"Mine!" She demanded, as Tom set her down. She crawled to the nearest toy and swiped it away from her grandmother. Tom chuckled as B'lanna walked in from the bathroom, in a clean uniform and looking a little less worn than before.

"Tom, how are you doing?" B'lanna asked. Tom shrugged.

"Well, better now I know what you've been doing over the last month." Tom replied.

"I'm sorry I couldn't tell you Tom. I wanted to, but I couldn't risk anyone spying or overhearing." B'lanna told him, almost as if she was seeking forgiveness. Tom smiled, walked over to her and kissed her gently on the lips.

"B'lanna, you don't need to apologise. I understand." Tom said. "You did the right thing."

"So you're not upset?" She asked him. Tom smiled, and shook his head.

"No, I'm not. Hell, I might have done the same thing." Tom said. He smiled at her, and kissed her hand. "At least now we're together here and we know what we're doing."

"Thanks Tom, that means a lot." B'lanna admitted. Tom raised his hand and wiped a tear away from her.

"How about dinner?" Tom suggested.

"Sounds good." B'lanna agreed. "But we need to go to the briefing room first."

"Mom, can you..." Tom started, but his mother held up a hand to silence him.

"Go on, get going. Miral and I will be fine." She said. Tom smiled, and took B'lanna by the hand, leading her out of their quarters and down the corridor.

Kathryn smiled as she looked at the crew working as hard as they had ever done, and she was proud of them. They had done a lot for years, and now were going above and beyond. Of course, she knew what they were made of, and what they could do. She walked through the corridors of Voyager, and smiled at the crewmembers she passed. She saw the determination in their eyes, and felt proud of them, of her family. As she walked onto the bridge, Harry stood up and smiled at her. "We'll be arriving at the Karandis system soon, Captain." He reported.

"Very good, Mr. Kim." Kathryn said.

"May I ask a question?" Harry asked, as Kathryn walked over to the centre seat.

"Always." Kathryn said.

"What's on Karandis?" He asked. Kathryn smiled.

"Nothing. We're staying there for a few moments and deploying a beacon to give off a false reading. If anyone does manage to follow our trail, they'll think that we are hidden somewhere on the planet, at least long enough for our warp trail to dissipate." Kathryn explained.

"Makes sense." Harry said, as he went to his station.

"Oh, and Harry?" Kathryn said.

"Ma'am?" Harry asked.

"I'm sorry about your promotion." She added. Harry smiled at her.

"To be honest, as long as I'm with you and this crew, I'll always be known as Ensign Kim. I think I was a little too eager. After all, what does a promotion bring me?" Harry asked. "I'm still where I want to be and who I want to be with."

"That's an extremely mature line of thought Harry. I'm proud of you." Kathryn said. She stood up as the senior officers came onto the bridge. "Briefing room." Kathryn said. She led the way, and everyone followed her, taking their seats. Kathryn stood at the head of the table, and looked at them. "I know this is proving to be a very complicated mission, but you need to know what happened to bring us here. Chakotay?"

"Five months ago, after the debriefing, Seven was doing some research on Starfleet when she came across a number of extremely secure files. She came to me since they seemed to be attached to files related to Voyager. After doing some digging, we came across a number of encrypted logs which showed orders to aid the government on Maldornia Three, shooting down a rebellion because someone in command wants to have them as an ally. Innocent women and children died at the hands of Federation weapons, although it was kept hidden. We did a few more investigations, and we found a number of other incidents just like it. We realised that Starfleet was becoming more of a military group, with more warships to be built. Finally, we came across files relating to the Federation Council, with Starfleet taking command. We needed to get out, and quickly, so we came to Captain Janeway." Chakotay said.

"After they did, I spoke with the Doctor whilst Admiral Hawthorne came to me, and he spoke to me whilst the Doctor was hiding in my office. He attacked me, and the Doctor stopped him. Scanning him, we found something we couldn't explain." Kathryn said. She pressed a button and a small image of a creature appeared on the screen. "I did some research, and some years ago, the Enterprise D discovered a conspiracy in Starfleet involving some sort of creature. We think that the same creatures have returned and somehow taken over Starfleet. According to the records, there was a tell tale sign of a part of the creature protruding from the back of the neck. This time, however, there doesn't appear to be the same sign." Kathryn continued.

"Surely someone will notice though?" Harry asked.

"I wish that was the case Harry." Kathryn said.

"As soon as someone realises what is going on, they're taken control of. From what we gather, Starfleet Command is pretty much under the same influence of these aliens, so we don't know who we can trust." Chakotay said.

"Have you spoken to Captain Picard?" Tom asked.

"Not yet. If I was the alien leader, I'd have gotten the Enterprise under control right away, especially since they foiled them once before." Kathryn told them.

"So what do we do first?" Tom asked.

"We're going to go to the Badlands. There are a number of former Maquis who were imprisoned by the Cardassians and who were released at the end of the Dominion War. I've made contact already, and they've already assembled whatever ships they could get their hands on. We'll be leading them." Chakotay said.

"So we're Maquis now?" The Doctor asked.

"No, the Maquis are now a part of Starfleet. We may be going against Starfleet, but we are the true Starfleet, and we've enlisted them. Their leader is a man who has had a lot of experience in Starfleet, and he's agreed to join us. We'll try and recruit as many ships as we can, but we need to find the base of operations. We know it won't be on Earth, and if we can take out their leaders, there is a chance the rest will all die." Kathryn said. "Any questions?" She added. When no one said anything, she smiled. "I want to thank you all for your trust in me. Now, before we go, we have one more important thing to do." She said. She stood up, and walked past Chakotay, who handed her a small box. Walking over to Harry, she smiled at him, and motioned for him to stand up, which he did. "We've all seen Harry grow from a green Ensign to a very experienced officer who is far more mature and skilled than many in Starfleet. For his exemplary service over the past seven years, and for his dedication, I'm promoting Ensign Harry Kim to the rank of Lieutenant, with all the rights and privileges therein." Kathryn said, opening the box and removing the rank pip and placing it on Harry's collar, much to his shock. Everyone began to clap and cheer, and smile at him.

"Congratulations Harry. You deserve it." Chakotay said, standing up and patting him on the back.

"T...thank you Captain." Harry said, smiling. "All of you, thank you."

"Your promotion is well deserved, Lieutenant Kim." Tuvok added.

"Now, sorry to cut the celebration short, but we need to get back to work. We'll have a proper celebration when this is over." Kathryn said. They smiled, and patted Harry on the back, before leaving the briefing room, soon leaving Harry alone with his thoughts.

"Lieutenant Kim." He said softly. "So why does this still feel wrong?" He asked himself. He shook his head, and put a smile on his face, turning and leaving the briefing room.

_Okay, I really want to thank you all for your reviews so far. Now you have an idea of who the bad guys are...or do you? Mwah ha ha ha ha..._

_Also, to clarify, in case there was any confusion, in Chapter 2, Reg was dreaming at first, he isn't in a relationship with Deanna, I wouldn't do that to Will Riker, heh. Please do give me your views and comments, I value them. I'll try and get more done today._


	6. Chapter 5 - Danger from Within

The bridge of the Enterprise was darkened as the ship remained stationary at the Tigris Nebula, after Captain Picard had to hide to make repairs. He sat in chair, looking at the crew around him. Even Data, normally unshakable, looked a little worse for wear, and Picard knew that he didn't even have his emotion chip activated. Two hours after leaving Earth, a number of crewmembers had begun to attack others in the ship, doing something to make them fight against the rest of the crew. Finally, after three hours, Picard and his officers had won, but a lot of damage had been done. Picard looked at Deanna's chair, which had a massive phaser burn on it, along with blood which had yet to be cleaned off. He shook his head, and stood up as the doors to the turbolift opened, with Will Riker stepping through it. "Captain, Commander Daniels and I have confirmed the prisoners are secure, and Doctor Crusher has submitted the final count. We lost thirty three crewmembers on our side, fifty seven on their side." Will said.

"Damn it. That's thirty three too many Will." Picard said.

"I know Jean Luc. I'm as angry as you are, if not more so. Deanna and I are due to be married next year, and now because of this, we don't know what will happen." Will said. Picard nodded.

"I'm sorry Will. I promise we'll get you both to your wedding." Picard said.

"I hope so. I know we seem to be the ship of miracles, but I'm tempted to go back to Baku, let time slow down." Will said. "I just hope Deanna can get through this."

"Deanna is strong, Will. We all know that about her. Given everything that she's been through, it's made her stronger." Picard said.

"I know." Will said, as the turbolift doors opened again. "She'll be okay."

"I have to be." Deanna said, stepping onto the bridge. "I spoke with Beverly, and she said that Amy felt no pain in her passing." She said, referring to Amy Ryder, a Starfleet Counsellor that Deanna had been training, and who was a good friend of Deanna's.

"Deanna, how are the crew doing?" Picard asked.

"They're tense, some are scared, but most of them are confident that we'll come through this, especially given everything we've all been through." Deanna said. "I spoke to Geordi, he and Reg are making really good time with repairs, especially with Data helping. The problem is we'll be stuck here for at least another day."

"We need warp power as soon as possible. I want to send a message to Worf on Qo'nos, but we can't risk it." Picard said.

"Jean Luc, we'll be out of here soon. Our first concern must be to figure out what the hell is going on. Beverly should find an answer soon, I hope." Will said. "Speak of the devil." He added, as Beverly walked onto the bridge.

"Please tell me that you've found something Beverly." Picard said, standing up.

"I think so." She said, looking worn and tired, her usually tidy hair messy and sweaty. She had a cut on her forehead which had dried up, but it looked nasty. "I've run a series of sub-molecular scans on some of the dead crew that attacked us, and I've discovered something unusual. Every one of them seemed to have an unusual anomaly in their cerebral cortex. I found some sort of device in the part of the brain that controls thought and control, but I don't know where it came from. If I hadn't been looking over every inch of the scans visually, I never would have seen it." Beverly said.

"So someone implanted these people and they were compelled to betray us and Starfleet?" Picard asked. Beverly shrugged.

"It's certainly within the realm of possibility, but I've never heard of such a thing. Not even the Borg use technology such as this." Beverly replied.

"So the question is; who does?" Will asked. Picard frowned, shaking his head.

"There is something we're missing here, something Captain Janeway managed to discover. I just wish we could contact her for more information." Picard said. "This reminds me of the situation we faced back on the Enterprise D, back in our first year, do you remember the conspiracy that Walker discovered?" Picard asked. All of them nodded.

"I remember, but it can't be them, because none of the crew have the thing protruding from the back of their neck." Beverly said.

"But someone could have found some way to replicate what those aliens did." Will commented.

"I can't know for sure, not until Geordi and I have done a full scan on the thing we found in the brains." Beverly said.

"How long do you need?" Picard asked.

"I don't know. If Geordi wasn't so busy, we'd be done within a couple of hours." Beverly answered.

"Work as quickly as you can, and report in as soon as possible." Picard said, as Daniels entered the bridge.

"Captain, I've had my teams search the quarters of every crewmember that fought us, and so far, we've not found any clue as to what is happening. I've still got my teams searching though, just in case." He said. Picard nodded.

"Thank you Mr. Daniels." Picard said. He sighed and sat down as Beverly left the bridge. Picard tried to stifle a yawn, but Will saw it.

"Jean Luc, please go and get some sleep. We won't find out anything if you're too tired, will we?" Will asked. Picard couldn't help but chuckle.

"I'll be in my quarters. Wake me if there are any developments." Picard said. Will nodded, and watched as he left the bridge, then faced Deanna.

"Make sure no one disturbs him for at least eight hours, no less." Will said. Deanna smiled, and nodded.

"On one condition; in four hours, you go and get some sleep yourself." Deanna said. Will nodded, and kissed Deanna's hand.

"Whatever you say counsellor." Will said. She smiled, and kissed him gently on the lips. Will smiled and returned the kiss, until a cough brought them back to reality. They turned and smiled at Geordi, who was standing there with Data. "Geordi, Data, I want good news only, that's an order." Will said. Data looked at him, turned and went to leave.

"Data, where are you going?" Geordi asked. Data turned and faced them.

"Commander Riker ordered us to give him good news. Since we have none to give, I felt it would be best to leave the bridge to attempt to find some good news to give him." Data said. Geordi, Deanna and Will chuckled.

"Don't ever change Data." Will said.

"It is impossible for me to change, since I am an android, and built to a very specific set of specifications." Data said.

"Data, it was a figure of speech. You should know that by now." Geordi said. Data nodded.

"In fact I do. I was attempting humour to assist with our delivery of bad news." Data said.

"Good try." Will said. "So, what's the bad news?"

"We're still trying to get the warp core back online. Whatever those people did, they knew how to shut us down. I'm worried that we'll need to do a full restart of the main computer, but if we do that, we could lose a lot of information." Geordi said. "However, it may be our only option."

"Data, can you identify all the files that have been unaffected so far?" Will asked.

"I believe I can, however if you are about to ask me to copy them, we do not have enough storage space anywhere on the Enterprise." Data said.

"Geordi, when was the last time we did an automatic update?" Will asked.

"Last week...Oh, I see where you're going with this. We only need to duplicate any file made in the last week because the restart will take us to last week's update." Geordi said, smiling.

"Ah, an excellent suggestion Commander. We will need about two hours to copy and isolate the files before we can perform a complete system reset." Data said.

"Good, do it." Will said. Data and Geordi turned and left the bridge, and Will looked at Deanna.

"Nice job, Will." Deanna said.

"I do have my moments Deanna." Will reminded her, with a grin.

"Yes, you certainly do." She agreed, leaning in and kissing him. However, he felt a little uneasy, and as they broke apart, Deanna looked at Will. "Are you okay?" She asked.

"Just fine. Last time we encountered something like this, it took Worf and I together to help stop Dexter Remmick, and this time we don't have Worf." Will said. Deanna nodded.

"Maybe not, but we'll see Worf soon, and he'll be able to help you again." Deanna said. Will smiled.

"Yeah, I know." He agreed. He found himself yawning, and Deanna smiled.

"Go and get some sleep. I'll join you soon." Deanna told him. He nodded, and looked at the bridge.

"I'm okay. You go rest, I'll join you as soon as Geordi and Data are done." Will said.

"Promise?" She asked. Will smiled, and nodded.

"I promise." He said. Deanna nodded, turned and left the bridge, just as Data walked back onto the bridge.

"Commander, I am sorry to disturb you again, but I have had an idea." Data said.

"Data, we have a problem." Will said. Data looked at him, confused.

"Sir?" He asked.

"We need to take Deanna into custody." He said.

"May I ask why?" Data asked, confused.

"Because she isn't Deanna. She looks like Deanna, but it isn't her. She didn't know that it was the Captain and I who stopped Dexter Remmick last time. I said it was Worf and I, and she agreed." Will said. Data looked at him.

"Are you sure?" Data asked. Will nodded.

"I'm sure. Go and arrest her, do not let anyone stop you. Stun her and take her to sickbay." He ordered.

"Aye Sir." Data said, as he went and left the bridge. Will looked at the viewscreen, feeling even more anxious that ever.

"We don't have a hope in hell." He muttered as he looked at the nebula.

_I can't believe how quickly this is coming together. I want to thank you all for your reviews, and I promise I will do my best to never let you down. As always, I value your reviews and look forward to seeing what you all say about this._

_I know, I added a twist to the story, couldn't help myself._


	7. Chapter 6 - Emotions

Seven looked up at the stars in the sky, from the grassy field she was sitting on, alone. She had started the holodeck program...she couldn't remember how long she had just been sitting there, alone, watching the stars. She had a vague feeling that she had done this before, and part of her knew she had done it as a child. This time, however, on the holodeck, she felt...well, she didn't know how to express the feelings. She wanted to go to Sickbay and tell the Doctor to put her implant back in so she wouldn't feel the way she was feeling, but that would mean she would need to explain why to him, and then he would try and help her cope and deny her request. She just continued to stare up at the stars, not noticing anything else around her, nor anyone else. She didn't even notice when Kathryn walked over to her and sat down next to her. "I used to do this when I was a little girl." Kathryn said.

"What?" Seven asked softly.

"Dream of a way to escape. I often messed up at home, and I'd always want an escape." Kathryn said. "At least, for a while anyway, until I faced up to whatever was making me feel that way."

"It is different in this situation." Seven said.

"Yes, I imagine it is." Kathryn agreed. "Seven, did I ever tell you about Mark?"

"You mentioned him briefly once." Seven replied. Kathryn nodded.

"I met him when I saved his life on Mars when we were young. When we got engaged, it was one of the happiest times of my life, because I never thought I would be able to love again, not after my father and my fiancé were killed in a shuttle crash." Kathryn said, regarding her friend. She took a deep breath. "For me, the hardest thing was that I had spent so much time waiting for the chance to be reunited with him. But when we made contact with Earth, I found out that he had married someone else, because he thought I was dead." She continued. She looked up at the stars, and allowed a tear to roll down her cheek. "At first, I was furious with him. I had waited for him, why didn't he know I was still alive? After all, I had faith that he was alive, and he should have felt something. I think, for the longest time, I just wanted to be angry at him forever."

"When..." Seven started, and then cleared her through. "When did that change?" She asked, feeling a tear of her own rolling down her cheek.

"It wasn't for a while, because when you're in love, it isn't something you can get over. I've never told Mark this, of course. We talk, and we're still friends, but I've never let him see how much he hurt me." Kathryn said.

"Why not? Could he not have healed your pain?" Seven asked, knowing what Kathryn was trying to say to her, but also appreciating the conversation.

"Seven, we never want the person who hurt us to see how much they have hurt us. I don't know what happened with you and Chakotay, but I am sorry that you're hurting." Kathryn said softly.

"How did you know we had ended it?" Seven asked. That question had been nagging at her for a while now, since the conversation had started. Kathryn flashed her friend a warm smile.

"Seven, I know my crew and I know everything that happens on this ship." Kathryn replied. She took a deep breath. "And when my friend is hurting, I know what to do to help, and also the cause of it. You are a part of my family, Seven, and when you're hurting, I'm hurting. That's what friends do." Kathryn said. Seven looked at her.

"Ever since the removal of my implant, I have been...feeling emotions in more depth, and it has been hurting. I...I am more hurt because I thought I loved Chakotay, and I think I did, but he...he does not love me." Seven said.

"Seven, how could he not love you? Don't you remember what the Admiral said? You and he were to be married. He would not have married you if he did not love you." Kathryn reasoned.

"But that is another Seven of Nine and another Chakotay. Our lives are different, especially since we returned to the Alpha Quadrant. If we had not returned, then perhaps I would have married Chakotay. But here, everything is different." Seven said, the raw emotion in her voice evident. "He needed to be free to follow his heart."

"Oh Seven..." Kathryn said, placing a comforting arm around her shoulder. "You are one of the most loyal friends I have known. I envy how you are able to do what is right, no matter the cost, without hesitation. If there were more like you, then perhaps life would not be so bad."

"Perhaps." Seven agreed, with a nod. "But it is what it is. Life is...complicated. I can understand why the Collective does not nurture emotions, they are not productive to a work environment."

"No, but they are necessary. After all, if we could live without emotions, things would be easier. But we would be empty, hollow rooms, dark and musty. Without our emotions, we may as well be dead. It is our hearts that guide us Seven, and yours will guide you to the one who will help you heal." Kathryn said.

"Do you truly think so?" Seven asked. Kathryn nodded.

"I know so." She promised. She stood up and looked down at Seven. "I need your help in the science lab. Care to join me?" Kathryn asked. Seven thought for a moment, and stood up.

"I will assist." Seven said. Kathryn nodded, and led her friend to the exit. Seven paused, looked back, and closed her eyes. "Computer, End program." She ordered. As Seven and Kathryn left the holodeck, one thing played on Seven's mind, one single word...

"_Alone..._"

_Thank you, all of you who are following my story. Already I can hardly believe how many people are following it and how many of you like it. I hope you like this new chapter, I even found myself crying for Seven and Kathryn as I wrote it..._


	8. Chapter 7 - Who to trust?

Tuvok looked at the reports that he had gathered before he left Earth, and so far, he had not found anything to show who was behind the takeover of Starfleet Command. Although he would not admit it, he was feeling frustrated at the lack of evidence and information. In his experience, criminals always made an error, and so far, he had yet to find it. He had expected to find some sort of outside communication, a stray message here or there. However, whoever had infiltrated Starfleet was good at covering their tracks. ~_Unless...~ _He thought. An idea struck him, and he remembered a conversation he had overheard whilst at Starfleet Engineering with B'lanna. He knew it would be risky, so he would need to seek permission first. "Tuvok to Janeway." He said, tapping his comm. badge as he looked at the nebula outside the window in his quarters.

"_Go ahead Tuvok._" Kathryn's voice said.

"Captain, I may have a potential lead but I need permission to contact Deep Space Nine." Tuvok said.

"_Can you mask your communication trail?_" Kathryn asked, although she already knew the answer.

"Yes, I believe I can." Tuvok replied.

"_Very well. Keep me informed, Janeway out._" She finished. Tuvok began to encrypt a communications channel, and then opened a channel to Deep Space Nine. He only had to wait a few moments before Colonel Kira Nerys appeared on the screen. He had met the Colonel when Voyager had returned to the Alpha Quadrant as she had been on Earth for a meeting with Starfleet Command.

"_Commander Tuvok. I just finished looking over a communication from Starfleet Command saying that you and your former crew had stolen the USS Voyager. Is that true?_" Kira asked.

"Indeed it is true, although we did so for a good reason. We have reason to believe that Starfleet Command has been infiltrated by an enemy presence." Tuvok replied.

"_What makes you think that?_" Kira asked, frowning.

"If I had more time, I would explain it, but right now, all I can say is that the Federation is in danger. I need to speak with Dr. Bashir, if that is possible." Tuvok said. Kira looked at him.

"_I received orders from Starfleet telling me to report in if I had received any communications from Voyager or the Enterprise. However, we've been having some communication errors, and we can't keep track of anything right now._" Kira said, with a sly smile.

"Thank you, Colonel." Tuvok said. Kira nodded and the screen went blank for a few moments before it changed again to show Dr. Bashir. "Dr. Bashir, I need your expertise. What do you know of a group called Section 31?" Tuvok asked.

"_A fair bit, I'm sorry to say. Why, what's happened?_" Julian asked.

"Starfleet has been infiltrated by a hostile force, and I believe that Section 31 is either behind it or a pawn of whoever is behind it." Tuvok explained. Julian frowned for a moment.

"_Are you sure? I mean, we took out one of their top men, Sloane, but we've not heard anything else. Starfleet Security were supposed to be looking into this group, but they never told me what happened._" Julian explained.

I do not have an explanation at this time. However, I need to know anything you may know of them." Tuvok stated.

"_Well, they don't keep records, but before Sloane died, Chief O'Brien and I used a device to enter his mind. He kept thinking of a name, but I never found anything in the Starfleet database of any officer with the name Alexander Archipelago._" Julian said. Tuvok thought for a moment.

"You would not. Alexander Archipelago is not an officer. It is a breed of wolf from Earth. An extinct species now, they were known as Canis Lupus Ligoni." Tuvok explained.

"_What does that mean though? Does it mean anything at all?_" Julian asked.

"I am afraid that I do not know, not yet." Tuvok said. "However, I have more information than I had before. Thank you Doctor." Tuvok added.

"_Anytime. If it helps, I'll speak with Colonel Kira and see if she can get Chief O Brien here so we can try and help. If the Federation is in danger, then Colonel Kira will be the first to help you._" Julian said.

"Very well. I will contact you in twelve hours to discuss this further. Tuvok out." He said, before closing the channel. As he did so, he thought for a few moments more, trying to determine the significance of the name.

"There is still no sign of them, and we have lost all trails of Voyager and the Enterprise." A male voice said, looking at the screen at the man on it.

"_Of course there isn't. Captain Janeway is very resourceful, I believe I told you that already._" The figure said.

"I have an idea, if I may? What if we were to contact the Romulans? After the Dominion War, they may be more than willing to preserve an alliance with us." A second man said. The room was well lit, but held one screen, one long conference table and twenty chairs around it.

"_Perhaps. For now, however, we must continue with our plans before we are discovered. How is our guest?_" The figure asked.

"He is still sedated, but we will leave him that way for now. At least he is easy to deal with in this state." A third man said.

"_Just make sure that he is not harmed. He will be our greatest bargaining chip. Keep him safe and comfortable. If Voyager come after us, we can use him to help stop them. There is one weakness that Janeway has; she cares for her crew, and for their families._" The man said firmly. He then closed the channel, leaving the men alone.

"Go and check on him." The first man ordered. As the second man nodded, he stood up, turned and left the room. Heading through their hidden base, the man smiled, knowing how well everything was progressing. He made his way into another room, and looked at the prisoner in the cell, who was just waking up.

"Who are you?" The prisoner asked.

"It does not matter who we are, Admiral, just what we will do." The man replied.

"And what's that? Attack and kill anyone who doesn't follow you?" He asked.

"In time, perhaps. For now, we will find and destroy Voyager, including your son, Admiral." The man said, looking into the clearly angry eyes of Admiral Owen Paris...

'Admiral Paris' stepped off of the turbolift on Voyager, and saw Kathryn. "Kathryn, have you had any luck yet?" He asked.

"Not yet, sir, but we will, don't worry." Kathryn replied, smiling. 'Owen' returned the smile.

"That we will, Kathryn." He agreed. "That we will."

_Dun dun dun...Yes, another twist, because I love them. Please do keep the reviews coming, I love them too :)_


	9. Chapter 8 - Revelations and Questions

Jean Luc looked at Will with a look he rarely gave the man anymore, the one that said ~Have you lost your mind?~ and for the first time, Jean Luc felt that he actually had to ask the question. "Will, have you lost your mind?" Picard asked.

"I wish I had, Jean Luc." Will said, as they stood outside the brig, where Deanna was now residing. "I know that's not Deanna, I know her all too well. She kissed me on the bridge, and she agreed with me when I said it was Worf and I who stopped the conspiracy." Will explained. "And I know when it's Deanna and when it's someone else." Will added. Picard nodded thoughtfully.

"Alright, let's say she isn't Deanna, who is she?" Picard asked. Will shook his head.

"I don't know. She does a very good impersonation of Deanna, but it's just..." Will started, trying to find the right words.

"Damned frustrating." Picard finished. "Alright, let me do the talking Will."

"Jean Luc, I..."

"I can make it an order if I have to, Will." Picard said. Will closed his eyes for a moment, nodded and let Picard lead the way in.

"Captain? Will? Why did you have Data put me in here?" Deanna asked, sounding confused.

"Save it. We know you're not Deanna Troi." Picard said bluntly. "I want to know who you are and where Counsellor Troi actually is."

"Captain, I don't understand. I am me." Deanna said.

"Counsellor Troi wouldn't have forgotten that it was Commander Riker and myself who stopped the conspiracy before, not Worf. Counsellor Troi would also not be prone to displays of affection on the bridge, especially not during a crisis time." Picard said. "I will ask you again; who are you?" He demanded. Deanna sighed, and stood up.

"We are here to help you." 'Deanna' said. "We were trying to get aboard the USS Voyager, but your ship was the first we could reach. Because of the conspiracy at Starfleet Command, we could not be sure who to trust. Your counsellor Troi is unharmed, I promise you that. You will find her in your morgue, under sedation." She added. Will looked at Picard, who nodded, and with that, Will left the brig.

"So who are you?" Picard asked.

"I am not able to tell you, but I do wish to help." 'Deanna' said. "I have been given an urgent mission. You must let me help you."

"Must we? How can we even trust you? You won't tell us who you are." Picard replied.

"Captain Picard, if I had meant harm upon you and your ship, I promise you that you would not be here now. We have come to honour an agreement that we made. We will help you, but we must find the USS Voyager. That ship is the key to everything, not only to finding out who is behind the conspiracy, but also to stopping the downfall of the Federation." Deanna said, as Will and the real Deanna walked in.

"Captain, I don't know much about our guest, but they explained everything to me before they sedated me." Deanna said.

"They?" Will asked, confused.

"Yes, we have someone else heading to Deep Space Nine, to attempt to make contact with your people there. We have learnt a lot of your conspiracy, but until we are all together I am unable to explain further." 'Deanna' said. Picard looked at Deanna, who nodded.

"Captain, she is telling the truth, as far as she believes it." Deanna said. Picard frowned and then looked at the two officers with him.

"And as far as we know, she made no hostile moves against the ship or crew, unless you count locking Deanna in the morgue." Will added. Picard nodded, and looked at the imposter through the forcefield.

"For now, you will be held in guest quarters, under armed guard. If you make any hostile movement, you will be considered a dangerous enemy and treated as such, understood?" Picard demanded.

"Of course, Captain. I promise you that I will make no attacks against your ship, and I will help in any way possible." 'Deanna' said.

"Do you have a name?" Will asked. 'Deanna' shook her head.

"Not one you can pronounce. However, so you don't get confused, you can call me Elizabeth. It is a name that I have heard and like." She said. Picard nodded, and looked at the guards, who lowered the field, but kept their weapons primed. As Elizabeth was led away, Picard looked at Will and Deanna.

"Do either of you have any ideas?" Picard asked.

"Right now, I'm still trying to decide if we're on a holodeck or if I'm having a really crazy dream." Will said, frowning.

"I know how you feel." Picard agreed.

"I think we should speak to Reg. Until we find Voyager, he is the foremost expert we have on the ship and crew." Deanna said. Picard nodded.

"Good idea. Deanna, you speak to Reg. Will, you and I will start searching for Voyager. As soon as Geordi gets warp drive back online, we'll head to Deep Space Nine, and meet the assistant that our guest has." Picard said.

"If only finding Voyager was going to be so simple." Will said.

"You think this is going to be simple?" Picard asked, raising an eyebrow.

"Figure of speech, sir." Will said. Picard smiled as the three of them left the brig.

"I...I...I'm sorry Deanna, I...I...I don't know why Voyager would be linked so much to this thing." Reg said, as he continued to pace his quarters, as he had done for the last several hours.

"Think, Reg, this person seemed to think that Voyager was extremely important. You weren't with them but they took you into their family, so they may have said something to you?" Deanna asked.

"If they did, I...I would have told you." Reg said, looking worried. "This...this is just like the time the Ferengi stole my hologram, using that woman."

"Reg, calm down. You aren't in trouble and this person almost had everyone fooled." Deanna told him. "We have to try and figure out who this person is and the agreement that they mentioned."

"Since the crew returned, they weren't on any official assignment." Reg said.

"So either it was unofficial or someone they met in the Delta Quadrant." Deanna said. She sighed. "Do you realise how those theories sound?"

"Yes...b...b...but I...don't see what else it could be." Reg said. Deanna nodded.

"Alright Reg. Now try and rest, you'd had a traumatic day." Deanna told him, standing up. He nodded as Deanna turned and left. She moved as quickly as she could towards the nearest turbolift. "Bridge." She ordered. She shook her head as the turbolift moved upwards, and as it did, she felt a growing feeling of unease welling up inside of her. As soon as the turbolift reached the bridge, she stepped out and went straight to Captain Picard. "Captain, I spoke to Reg, and he thinks that the agreement that the person mentioned was either someone unofficial, or someone from the Delta Quadrant." She said.

"Which gives us nothing since we can't track either." Will said.

"Maybe not, but I can search the Starfleet database and see if there are any species who can travel this far." Deanna said.

"Very well. In the meantime, Geordi says that we'll be warp capable within twenty four hours." Picard said.

"What if we can't...stop whoever is doing this?" Deanna asked. Picard looked at her, and then at the viewscreen.

"If we can't stop this..." He started, feeling his heart heavy. "Then we, and the Federation, won't have long to live."

_Again, thank you all for your reviews. I would like to address two points made by one reviewer, Mary S, because she made good comments. The first was about Miral being able to say the word 'Mine' and 'Dada' despite being six months old. I can say that I have heard six month old babies speaking, but because of her Klingon DNA, Klingon children tend to advance a bit more than human children, and there is an eventual explanation, not gonna say any more. As to the second point, I thought I had heard Will call him Jean Luc on the bridge before, but I could be wrong. _

_I enjoy comments such as those because it helps me know where to improve and grow better as a writer, so thank you all for your comments. I love you all for being my inspiration to write this story as fast as I have._


	10. Chapter 9 - Uneasy Alliances

As Voyager dropped out of warp on the edge of the plasma storms that the badlands was famous for, Kathryn, along with everyone else on the bridge, suddenly felt a wave of fear wash over them which abated quickly. The last time Voyager had been at the plasma storms, the Caretaker had sent them to the Delta Quadrant. This time, however, the Caretaker was dead. "Mr. Paris, take us in." Kathryn ordered.

"And if you detect a coherent tetryon beam scanning us, get us away from here quickly." Chakotay ordered, eliciting a small chuckle from the bridge crew.

"Nervous Commander?" Kathryn asked softly.

"A little. Aren't you?" Chakotay asked. Kathryn nodded.

"Well, the last time we were here we began a long journey to get home. In a sense, we're doing the same thing again." Kathryn said.

"Kathryn, we're going to save the Federation. With you leading us, we can't fail. After all, you got us back home before." Chakotay reminded her. Kathryn nodded as Voyager flew between the plasma streams, with Tom expertly avoiding them. "Tom, Delvas Three is our target. According to my contacts, we'll meet them there." Chakotay said. Tom nodded, and as Voyager turned, Harry looked up.

"Captain, we're being scanned by something." He said, frowning. Both Chakotay and Kathryn stood up, and faced him.

"By what?" Kathryn asked.

"I'm not sure. I'm trying to track the source now." Harry replied.

"Tuvok, raise shields. Tom, on my command, get us out of here." Chakotay ordered.

"I've localised the source of the scan. It looks like a Federation Starship, but with no identification code being transmitted." Harry said.

"On screen." Kathryn said. The screen changed to show three Starships facing Voyager, one Constitution Class refit, an Excelsior Class and an Ambassador Class.

"Any identification?" Chakotay asked.

"I am unable to scan them properly in this area of space. However, there appear to be markings on the saucer sections." Tuvok said. He zoomed into the Ambassador Class and frowned.

"Is that the name I think it is?" Kathryn asked.

"Yes, it's the Val Jean A." Chakotay agreed, staring at the ship. "I...I think we found the Maquis. Why they called it that though..."

"The Val Jean is hailing us." Harry said.

"Onscreen." Kathryn ordered. The screen changed to show a face that they all knew, although Chakotay suspected that he knew the person better than Kathryn did.

"_Captain Janeway, I'm Captain Riker of the Val Jean._" Riker said.

"Captain Riker? I hadn't heard of your promotion. Is the Enterprise around here?" She asked.

"No Kathryn. That's not Will Riker, that's Tom Riker, his twin. Good to see you Tom." Chakotay said.

"_And you Chakotay. I trust you like the name I chose?_" Tom asked.

"It's certainly unexpected. Where did you get the ships from?" Chakotay asked. Tom smiled.

"_Since the Dominion War ended, Starfleet was selling outdated ships to the merchant fleet to help ensure that the Cardassian's and others affected by the war were able to receive supplies. We posed as a merchant group using latinum that had been stored and hidden and were able to have them refitted, although we could use some help with some of the systems. Starfleet stripped out the weapons, sensors and communication systems. We were lucky that they left the warp core in._" Tom said. Kathryn looked at the screen.

"One moment please Captain." Kathryn said. She nodded to Tuvok, who closed the channel. She looked at Chakotay, and he knew that she was both concerned and suspicious. "Okay, I know we're pretty much into the unusual at the moment, but this...something feels wrong. I don't know if we can trust this Tom Riker. Was he in the Maquis?" Kathryn asked. Chakotay nodded.

"He has the same sense of moral guidelines that Commander Riker has, he just has a different outlook on life since he spent eight years alone on a planetary Starbase." Chakotay said. "I've worked with him, and I trust him." He added softly.

"Alright Chakotay, as long as you trust him." Kathryn said, nodding.

"I do. I'll stake everything on it." Chakotay said. Kathryn nodded, and faced the screen again, just as Tuvok opened the channel once again.

"Captain, we should be able to help you. If we can go somewhere safe we can discuss the situation in greater detail." Kathryn said.

"_We have a base at Delvas Three we can use. I should warn you that it isn't exactly...legal, but we were able to, shall we say, procure it for our use, without the original owners knowing._" Riker said. Kathryn nodded.

"Lead the way." She said. "Voyager out." She added. As the three ships on the screen turned around, Kathryn looked at Chakotay. "I really hope you know what you're doing." She said.

"So do I." Chakotay admitted.

As Voyager entered the Delvas system, Kathryn couldn't help but feel exceptionally nervous as she watched the screen eagerly. "I am detecting at least twelve ships of the same class that the Maquis used to use, as well as a larger power source, possibly from a Starbase." Tuvok said.

"But the Maquis never had the resources for so many ships and especially not for a base. Someone has had to have been helping them." Chakotay said.

"Who would have that much gold?" Tom asked.

"I have a visual on their Starbase." Tuvok reported.

"Onscreen." Chakotay ordered. As the Starbase appeared on the screen, Kathryn frowned.

"That's obviously not the one we think it is, right?" She asked.

"No, it can't be." Chakotay agreed.

"Captain Riker is hailing us." Tuvok reported. As Kathryn and Chakotay faced the viewscreen, Tom Riker had a huge grin on his face.

"_Captain Janeway, Commander Chakotay, welcome to Liberty Base._" He said.

"Captain, your base...it certainly is impressive. Where did you get it?" Kathryn asked, fighting hard to keep the shock off of her face.

"_We came across it abandoned a few years ago, and we decided to convert it for our own use. We were able to bring it here, using a lot of...effort and assistance, and we cleared it out fully, securing it and making it ready to be opened fully. The Maquis may not be needed to fight the Cardassian's anymore, but we're preparing to make ourselves a fully fledged government._" He explained.

"Impressive. Do the Cardassian's know you have their base?" Kathryn asked.

"_They abandoned it years ago due to a science experiment that went wrong. The station was used several times but never found a proper use. Now we are attempting to fully arm and power up the station, and any help you can give would be welcome._" Riker said. Kathryn's frown, and feeling of unease, grew deeper.

"And who is leading your movement?" Kathryn asked. Riker looked at her, smiling.

"_Actually, the ship Captain's have been leading, although we all decided on a leader we wanted._" Riker said. He then looked at Chakotay. "_Who better to lead us than Chakotay, from what used to be known as Empok Nor?_"

_Sorry that I only got one chapter out today, I had hoped to write more but it's been hectic. First, thank you to all of you who pointed out that Riker only calls Picard by his first name when off duty and not on the bridge. At some point soon, I will edit and rectify the error, and make sure that I don't make the same mistake again._

_Please keep reviewing, and I have to say I am so thrilled that so many people are enjoying my story. I hope you all continue to enjoy it._

_Also, as a thank you, if you are members of this wonderful site, please inbox me after reviewing as I need some names for Captain's in the New Maquis Fleet, and would be happy to name some characters after you wonderful people :)_


	11. Chapter 10 - Command Decisions

It was safe to say that in all her years in Starfleet, Kathryn Janeway had never felt as uneasy as she did when she sat down in the war room of Liberty Base. Chakotay and Tuvok were with her, along with B'lanna, especially since B'lanna and Chakotay had been senior members of the Maquis. For his part, Chakotay had never felt as apprehensive either. The Maquis had survived, and now he was being asked to lead them again, and once more it was in a battle against tyranny and oppression. He wanted to speak to Kathryn in private, but they had to attend the meeting. Kathryn took a look at the people who were present, waiting on Tom Riker. Captain Janette McKay was the Commanding Officer of the Station, and next to her was her first officer, Commander William Dawes. Chakotay had met Janette several times before, but never for a long period of time since she had once been a ship commander, like him. He missed his ship, the original Val Jean, named from an old Earth play. He smiled as he remembered the crew, and how most of them were aboard Voyager now. Next to McKay was Captain Rhonda Delaware, who was, for the time being, without a first officer. He smiled when Kathryn put a hand on his, which was gently tapping the table. "Chakotay, it's going to be alright. We'll figure this out." Kathryn said. Chakotay nodded and went to reply when the doors opened, and Captain Riker walked in, followed by a Romulan Officer, who looked to be deep in thought.

"Thank you all for coming." Tom said. He looked around the room. "This is Commander Bochra. He's our liaison with Romulus. Whilst they can't publicly support us, there are those who wish to help us." Riker said.

"My job is to call in for assistance and supplies as I deem fit. I was given this assignment because Commander Tomalak recommended me after I encountered the Enterprise D and formed a friendship with Commander Geordi La Forge." Bochra explained.

"So where are you getting the finances for this whole operation?" B'lanna asked. "Don't tell me you had a lot of gold latinum saved up somewhere." She added.

"No, we have had some...financial backers, very wealthy ones." Riker said. "I'll get to that. For now, I'd like to explain how this whole situation came about."

"That'd be nice." Kathryn said. Riker nodded and took a deep breath.

"When the Maquis were almost wiped out, several thousand were taken as prisoners, men, women and children were all taken to labour camps. Near to the end of the war, we were moved to a facility which was going to be used to build a new weapon. However, Captain Sisko led the attack which ended the war, and a Cardassian named Garak was named to lead the union, after it was revealed that not only was he the man who helped free Cardassia, but he was the son of Tain, a man who was very well respected. He had always understood why the Maquis did what they did, and ordered our release. He even had ships provided for us to leave to wherever we wanted to go, and supplies. It didn't make up for being imprisoned and tortured, but it was a sign that the Cardassian's that we had been attacking were no more, it was a new, more humble Cardassia. We accepted the supplies and made our way here, where we set up a new base." Tom said.

"About a year after we had set up the base, we found an old Maquis supply depot here, one which we think the leaders were hiding and were going to stockpile it in case we were all defeated and needed a fall back, but something happened and it was forgotten. We had weapons, and five ships, not to mention the unarmed Cardassian transports. And we needed them because almost a month later, we were attacked by pirates, although we're not sure where they were from. We defended ourselves, but we also attracted the attention of a Romulan Warbird that was tracking the pirates, commanded by Bochra, and he was able to help us build better defences. But we knew we'd need a lot more, so using a supply of latinum that we found in the stockpile, we purchased the three ships from Starfleet, and named them the Val Jean A, after Chakotay's ship, the Excelsior class we named the Hudson and the Constitution we called the Eddington. Ro Laren took command of the Hudson, and Captain Delaware took command of the Eddington." McKay said.

"Whilst I took the Val Jean for my ship. We managed to equip weapons onto the ships but we still were vulnerable. By that time, Bochra was assigned as a liaison to us, and when we were on a supply run, we found Empok Nor. We gathered all the ships that we had, and we towed it here, using a new shield modification to protect it from the plasma storms. Luckily, the Romulan's had been working on a new shield design to help traverse the plasma storms. She needed repairs, but we managed to get her repaired and armed, although not fully." Tom explained.

"We have about two hundred photon torpedoes and without access to a Federation Replicator, with the design codes for the torpedoes, we can't get any more." McKay added.

"We thought of asking for assistance, but then we heard rumours of problems in Starfleet, and we didn't want to risk it. We currently have no replicators at all, hence one of the reasons we need help." Tom said.

"And my government couldn't supply any equipment without it being noticed, especially by the Federation, so we were making do." Bochra stated. "We are desperate here, and we need help and experienced leadership."

"I don't know about the leadership part, but we can certainly help with the replicators. B'lanna, use whatever you need to in order to get their replicator systems working. We'll also help arm you, but our help comes at a cost." Kathryn said.

"Here it comes." McKay muttered. Kathryn chose to ignore her, although Riker shot her a look.

"First: You will not attack anyone except in self defence, unless I authorise it. No offence, but I need to know you and your people can follow our orders, especially if you want my help. We do things my way. Second rule is that you help us find out what is happening in the Federation. We need to find whoever is behind the conspiracy and put them down. Lastly, for now, you answer to me. This will be a joint effort, and I'll lead it, along with Chakotay. After we're done, then we'll discuss your leadership. If you have any problems, we'll leave now, understood?" Kathryn demanded. The Maquis leaders looked at one another, and nodded.

"We agree." Tom said. "And just so you know, this is all about freedom. After we're done, we're an independent government, and since you set your condition, I have a few of my own. One, you help us to become a fully fledged government in the eyes of everyone, included your vaunted Federation Council. Two: We want industrial replicators, and we want them right away. B'lanna can construct a few using your own replicators, I'm sure, but we need them. People are starving and we need to get them all fed." Tom said. "Finally, the Federation will make no hostile act against us. Yes, we once stole from Starfleet, but if you can forgive Chakotay, you can forgive us, especially given the risks we're taking." Tom stated.

"I can't guarantee all of that. I'll allow B'lanna to build the replicators. The rest...well, I will support you, but that's all I can do." Kathryn said.

"You could have lied and said yes to us." Bochra said, tilting his head, confused.

"We need you and you need us. I don't see the point of beating around the bush." Kathryn said bluntly.

"Alright, we have an agreement." Tom said, nodding. "Thank you."

"No." Kathryn said. "Thank you. Right now, you've helped give us some hope that we can save the Federation."

"Maybe they have." B'lanna said darkly. "But is it enough?"

_Again, this one is for my supports and fans, but a big shout out to byasouthernlady, who has been a fan from the start. Thank you :) And also, as usual, please do review. Thanks_


	12. Chapter 11 - Unveiled

As the Enterprise dropped out of warp, Picard frowned as he saw at least ten Starfleet vessels around Deep Space Nine, and he felt even more apprehensive than ever. Three of them were Sovereign Class Ships; there was a Nebula Class, an Excelsior Class, two Galaxy Class, as well as a Prometheus Class. The last ship was another Defiant Class ship, along with the Defiant herself. "Captain, all vessels have their shields raised and weapons armed." Daniels said.

"We are being hailed by the Defiant." Data reported.

"Onscreen." Will said, looking concerned. As Colonel Kira's face appeared, she looked at them.

"_Captain Picard, the fleet here is under orders to arrest you and your crew and escort the Enterprise back to Earth._" Kira reported.

"Colonel Kira, we are facing a dangerous enemy, one which we must join forces to defeat. A conspiracy is overtaking Starfleet." Picard said.

"_Starfleet contacted Bajor and asked for their assistance. Whilst Deep Space Nine is considered Bajoran property, the council agreed to assist with all of their might._" Kira said. She sighed. "_Which is why I had the weapons taken off line. We need a place to run. I suggest the Badlands, there are several places there which we can use to hide. The USS Sisko, the Defiant Class, is on our side, as is the Prometheus. Thankfully, they're commanded by old friends who trust me._"

"I will speak with the other Captain's. With luck, they are simply following orders and are not a part of the conspiracy." Picard said.

"_Good luck. We'll stay here until you give us the say so._" Kira said. Picard nodded, and looked at Data.

"Mr. Data, send a message to all the ships and invite the Captain's aboard, ask them to bring their first officer and a security team if they wish, but tell them we wish to speak with them, and if they are not satisfied with what I have to say, then they can arrest me." Picard said.

"And if they're not satisfied Captain?" Will asked, stepping forward. Picard sighed and tugged his jacket gently.

"We shall just have to hope they are." Picard said. "Number One, will you go and meet the Captain's and escort them to the briefing room? I'll be setting up. Mr. Daniels, please escort our 'guest' to the briefing room."

"Aye sir." Will and Daniels said. As they left the bridge, Picard thought for a few moments, about what he was going to say, and began to walk towards the briefing room.

"Captain, your story is...unusual. Were it any other Captain, I would certainly not hesitate to arrest you. However, your reputation for the unusual certainly gives you credibility." Captain Selok of the USS Antares stated.

"Thank you Captain." Picard said. "You all know me. I will take any test to prove that I am still me. I have seen things which, quite frankly, if I hadn't of witnessed them myself I would not believe it. But I come to you now, one Captain to another, and ask you to help me save the Federation." Picard said. Every CO looked at him. "I don't have answers, and we have a lot of suspects. But we need to find the source of this conspiracy quickly, or we don't have any chance of surviving."

"Well, we should just talk with them, send a fleet wide message and explain everything." Captain Andrew Sheridan said.

"I have been considering such a thing, and quite frankly, it could work, but we'd need to be careful not to allow the conspirators to know our location." Picard said, just as Data walked into the room.

"I apologise for the intrusion Captain, but we are picking up a signal being transmitted along every Federation news channel, and every Starfleet priority signal." Data said. Picard tapped in several commands into the panel in front of him, and an emergency news broadcast could be seen. It was a woman standing in front of the site of a massive explosion. In the background, Picard was sure he could see the Eiffel Tower.

"_Our top news story: Yesterday saw a dark day for the entire Federation. This report is being broadcast along the entire Federation News Network, and on all emergency channels._" The reporter said.

"What's happened?" Will asked, looking at the screen.

"_At oh nine hundred hours, Starfleet Security received an emergency call for help from the Federation Council chambers. Upon arrival, they found a lot of corpses, Starfleet Security officers and Ambassadors alike._" The reporter started, showing a visual from a Starfleet Security officer's visual recorder. It showed an armed team slowly walked through the lobby of the building, showing nothing but dead bodies, some visibly burnt from repeated phaser fire. There were some who looked like they had been cut up like they were nothing more than meat. Picard looked at the faces of the officers in the room, all of whom looked like they were going to be sick, except for Captain Selok and Captain Savok, CO of the Nebula Class USS Ozymandias.

"Who could do such a thing?" Sheridan asked.

"Our conspirators. We need to find them, quickly." Picard said.

"_One of the security officers was able to download the security camera logs. However, once the logs were transmitted, it is believed that they triggered a command implanted by the terrorists who were behind this._" The reporter continued. "_The entire building was engulfed by an explosion, killing thirty security officers and over three hundred civilians who were near to the area. It is believed that the death count is almost two thousand people._"

"We need to get to Earth, now." Captain Malcolm Richardson said, standing up.

"I don't think we're going to like this next part." Will stated.

"_After reviewing the security logs, the attackers were identified as Starfleet Officers, armed with phaser rifles. It appears as though they were led by Lt. Commander Data of the USS Enterprise. We are still trying to find out how he was able to leave Earth, but it is believed that he remained aboard when the Enterprise attacked the USS Drake, killing over seventy crewmembers. As for the escape, it is believed that the USS Ozymandias, which left Earth's space at oh seven thirty yesterday._" The reporter continued

"Okay, is anyone actually buying this crap?" Sheridan asked.

"I am certainly not believing this, especially since my ship now appears to be involved." Savok said. Picard could have sworn that he heard a hint of anger in the man's voice.

"_Starfleet had not released any details until recently, but they released a statement ten minutes ago._" The reporter said. The screen changed to show Admiral Warren Hayes, looking angry as he stood in front of a crowd of reporters.

"_After investigation, we can now confirm that the entire Federation Council was murdered. Every single member planet has been notified and a new council has already been formed. It's first act was to grant Starfleet emergency powers to help track down these terrorists and bring them to justice. After a thorough investigation, we know that these attacks were led under the command of Captain Jean Luc Picard and Captain Kathryn Janeway. There are others, including Captain Savok of the USS Ozymandias and Captain Andrew Sheridan of the USS Prometheus, who are believed to be following these terrorists. As of right now, we are declaring a state of emergency, and authorising lethal force on any ship under Picard's command. We have sent the list to every Starfleet vessel, and we have been informed by sources that they are working with Colonel Kira Nerys. The Bajoran Government has agreed to give Starfleet full jurisdiction and we have dispatched a fleet of ships to track down these renegades, believed to be at Deep Space Nine. We will track these murderous traitors down and we will bring them to justice. I ask you all to be careful. If you see the Enterprise or any ship under the command of the Enterprise, we ask you turn and run quickly, and alert the nearest Starfleet vessel._" Hayes said. Picard shut down the screen.

"It appears that the next move has been made. We need to leave, now." Picard said.

"And go where?" Kira asked, as they all stood up.

"I suggest we head for the Tigrin Nebula, we can hide there." Picard said. "Any objections?" He asked. When no one spoke, Picard stood up. "Alright, let's go, immediately. From here on out, we're not Starfleet Officers. We must go renegade to save the Federation."

"And stay dark. We can't communicate with anyone until we know what to do." Sheridan stated. Picard nodded and looked at them darkly.

"May fortune favour the bold." He said.

"Or the stupid." Will muttered, as they all left, leaving Picard alone, wondering if he would ever get to see Earth again.

_Okay, I hope I've given you an excellent twist here. If you have any questions so far please do message me. More will follow as soon as I can write more, but I might not get anything done this weekend, although I will try. Remember, please do keep reviewing so I know you like my stories :)_


	13. Chapter 12 - Matters of the Heart

(Five months later)

Chakotay walked onto the darkened bridge of Voyager, looking around at the almost empty bridge. Since the attack on Earth, they had not been able to leave the planet's Orbit, and were forced to utilise cloaking devices that had been given to them by Bochra, who had insisted they remain hidden otherwise everything they had been fighting for could be lost. Chakotay had taken Voyager out once a month to get more supplies, but it had been dangerous. Now, of course, they were docked with Liberty Base, waiting. That was what annoyed Chakotay the most, the waiting. Risking his life to help the others he could live with. But not the waiting, not even a little. He sat down in his seat, and looked at Tom, who, along with Harry, were the only people on the bridge. "Any news?" Chakotay asked.

"Nothing." Tom replied. He turned his chair around. "Chakotay, there has got to be something we can do other than just sit here." He said.

"We're going stir crazy doing nothing but waiting." Harry added.

"I know how you both feel. I'm not happy about it but we can't really do much. Every Starfleet ship has a shoot on sight order on us." Chakotay reminded them.

"Yeah, but the station is almost at full power now." Harry said.

"Yeah, almost." Chakotay reminded him. "Until it is, we're still vulnerable."

"Do you think we'll get out of this one in one piece?" Tom asked. Chakotay smiled.

"Of course we will Tom. We've gotten through worse scrapes." Chakotay said. "Remember the time we were stuck in the Void?"

"Or the time we were in the subspace pocket." Tom said, smiling.

"Or the Borg in the nebula." Harry chipped in.

"And look, we're still here." Chakotay said. "And I know Captain McKay and Riker, they're good people."

"I hope so." Harry said.

As she walked into her office on Liberty Base, Captain Janette McKay sighed and sat down, feeling the pressure of the day's events. Finally, the phaser banks were just about ready, but they still needed to get the torpedo launchers ready. She wished she could have had people from Deep Space Nine helping her, but she was glad for the help she did have. She looked up as her office door opened and Bochra walked in. "Are you okay?" He asked. She glared at him, her hair unkempt and sweat streaming down her face. "Okay, foolish question, you look like I did after Galorndon Core." He said.

"The day you first started to trust humans." McKay said. Bochra nodded.

"Indeed." He said. "You need rest. Go and sleep, and wash, and I'll look after things up here."

"I can't, I'm needed here." McKay said. Bochra smiled, leant over the desk and kissed her gently on the lips. He pulled back after a moment and smiled.

"Remember, in the grand scheme of things, I am the higher ranked officer." He said.

"By who's standards? You're only a Commander and I'm a Captain." McKay said. Bochra chuckled softly.

"Perhaps, but my ship and title are official. Yours aren't, not yet anyway." He reminded her. She looked at him, sighed and nodded.

"Fine, but you're coming with me, you need rest as well." McKay said. He smiled, and nodded at her.

"Alright, I'll agree to that." He said, holding out his hand. She took it and the two of them left together, letting themselves forget the troubles they were facing, if only for a little while.

As Kathryn sat alone in her quarters, she felt like she had let her crew down...again. Tuvok had spoken to her and told her that no one blamed her, but she still felt like she was to blame. But usually there would be a way to handle the guilt and the shame she felt. She stood up and looked at the station through her window. As she did, her chime rang, and she knew who it was. He came every day at the same time, like clockwork. "Enter." She said, not bothering to turn around. "Anything new to report, Chakotay?" She asked.

"I'm afraid not." Chakotay answered, looking at her. "We've been here before, haven't we?"

"Have we?" She asked, although she already knew the answer.

"You know we have. I'm not letting you do this again." Chakotay said.

"Chakotay, I'm not shutting myself away. Right now, I'm still trying to decide our next move." Kathryn told him. Chakotay smiled.

"Kathryn, this isn't your fault." Chakotay told her. "We've been stuck here for five months, I know you're feeling frustrated, especially having to stay behind on the station, but we're going to get through this."

"How are we?" She asked angrily. "Chakotay, they killed the entire Federation Council and I'm willing to bet that right now, the new council is under their control."

"I've been watching the Federation News Channel, as best I can." Chakotay said. He sighed as he walked over to the screen in her quarters and activated it. They watched as the new council leader, President Arnold Milton, spoke first.

"_Today, five months after the attack on the last Federation Council, an act of terrorism from within, it is proposed that we take direct control of Starfleet, and use the ships in Starfleet to protect our borders in more direct ways than before. We must not allow our enemies to control us. We must build our military forces and defend the Federation from all enemies, foreign and domestic. No more will rebels or terrorists be allowed to continue in our great Federation. No more will we be the victims. No, we shall be the leaders!_" Milton said, as everyone in the background cheered. Kathryn shut off the screen, and growled angrily.

"So this is how freedom is destroyed: by applauding fools." She said.

"Kathryn, what can we do?" Chakotay asked. Kathryn looked at him.

"I don't know. But we need to think of something, quickly, before we lose the Federation forever." Kathryn said.

"Then we should start contacting other ships, and make our way to Earth." Chakotay suggested.

"Like who? Most Captain's have brought this hogwash. Now we need to undo the damage done, but we don't have anything with which to do it." Kathryn said.

"We have you." Chakotay said, sitting next to her. "Kathryn, you and I have survived worse than this. We spent time on New Earth, we beat the Borg, the Hirogen and even the Viidians. We can stop this."

"I wish I knew how." Kathryn said, sitting down and looked at him. "Chakotay, you've been one of my closest friends for years. I think it's safe to say I've told you things I've told no one. I trust you with my life, so if you tell me we'll get through this, I'll believe you."

"Kathryn, we will get through this. The Federation is counting on us." Chakotay said, looking into her eyes, and smiling at her. He took her hand. "You'll lead us, and I'll be right there by your side."

"You've always been there for me." Kathryn said. She felt her heart beating faster, and wanted to lean in and kiss him suddenly. "I've always fought you, but you've never let me down."

"I never will." He promised.

"Can I ask you something?" She asked. Chakotay nodded, so she continued. "Why did we...never take things further?"

"How could we? You were a Captain determined to get us home, and I needed to keep you sane." Chakotay said. He smiled. "Besides, how would we have gotten anything done?" He joked. Kathryn laughed softly, and smiled.

"Thank you." She said. "I...I feel guilty though, having these thoughts...when you and Seven..."

"I think Seven knew about our feelings before we did." Chakotay said. "When she ended things with me, she told me that there was someone else I loved, and that I would know who it was."

"So do you love me?" Kathryn asked, finally asking the question she had wanted to ask for some time now.

"I have done for years now Kathryn." Chakotay said. She smiled, leant in and kissed him on the lips. He closed his eyes, and allowed the kiss to continue for a moment before breaking apart. "Not yet." He said.

"We need to complete this mission first, right? Stop Milton and whoever else is following him?" Kathryn asked. Chakotay nodded. Kathryn leant over and kissed him once more, then stood up and smiled. Chakotay also smiled, for he now saw a new light in her eyes, as though a fire had ignited in her. "In which case, they had better stand down now, because nothing will stand between us."

"And if they try?" Chakotay asked. She looked at him, a fire in her eyes that would scare anyone on her bad side.

"Then they'll answer to me!"

_I really hope you all like this chapter, I've been working on it all day. It is a chapter that will shape a lot of the story. Please do review it and let me know what you all think :)_


	14. Chapter 13 - Why does it hurt?

"Ah, Tommy lad, I don't suppose ye have a few bob for a pint do ye? I would buy me own but my beautiful wife, well, you know the sweet lass..."

"Let me guess, she took your money from you?" Tom asked Seamus, who tilted and shrugged his head as if to say 'yes' to Tom. Tom sighed, and handed some money to his friend.

"Ah, never a finer space man than you Tommy." Seamus said, grinning as the two men walked towards the pub.

"Is that because he paid your bar bill again?" A friendly voice asked from behind. Tom smiled as he turned and saw Michael Sullivan. "Tom, welcome back. It's been far too long since we saw you here."

"Thanks Michael." Tom said. "I was just looking for something to keep my mind occupied."

"Well, if ye like, we have a game of hoops starting shortly." Michael said, smiling. "Only rule is no using your fancy toys to cheat."

"I wouldn't do that!" Tom exclaimed, faking a sound of indignation.

"Tommy lad, next time you want to try and fleece an Irishman, you should make sure they can't hear you give an order to your computer." Michael said, smiling as he put an arm around Tom's shoulder. He looked shock, and then gave a small, sly smile.

"Fair enough. You can watch me the whole time." Tom said.

"I'll hold ye to that." Michael said. As they walked along, Michael looked at Tom. "So how's Katie doing?"

"She's...well, under a lot of stress." Tom said, with a nod. "I guess it's safe to say she's not handling things well."

"Well, maybe we need to get her down here for a game of hoops. She's pretty good as I remember." Michael said. Tom nodded.

"I agree, but trying to get her to leave her quarters is a challenge. I think she blames herself for the situation we're in." Tom said. Michael nodded.

"I heard, your friend Harry told me what's happening. Is there anything I can do to help ye out?" Michael asked.

"Well, I'll probably keep Fair Haven running for a while, give the crew a chance to relax a little. You might get a little crowded round here." Tom warned. Michael smiled.

"Well then, I'd best get to the brewery and order more ale." Michael said. Tom chuckled.

"You know I could do that for you in a second." Tom said.

"Glad ye volunteered. Come on, I'll show you where I need them." Michael said. Tom nodded, smiling, and followed the man.

As Harry walked down the beach, he frowned, seeing Seven sitting on the beach, alone. Seeing her in the holodeck was unusual enough, but in Fair Haven? Not something he had ever seen. He walked towards her, and looked down at her. "Seven, what's wrong?" He asked.

"Ensign Kim. Nothing is the matter." Seven said. He ignored her failure to address him as Lieutenant, at least for now.

"Really? You're here, on the beach, alone. Seven, I know you quite well, you don't sit alone. Well, you do but not on the beach." He said. She paused and looked at the ocean.

"I came because someone suggested that the waves would be pleasant to listen to. So far, I am not convinced." Seven said.

"Seven, I don't believe that for a second. I don't know what's wrong, but I'm here to help." Harry told her. Seven stood up.

"I do not require help from anyone." Seven said.

"Really?" Harry asked. "Seven, I'm your friend, I just don't like seeing you like this."

"Your concern is noted, Ensign." Seven said coldly, going to walk off.

"IT'S LIEUTENANT!" Harry snapped. Seven stopped, turned and looked at him. "I'm just trying to help. If you don't want my help, then fine. But I spent seven damned years on this ship as an Ensign, and I never got a promotion once. Now I have it, I'll thank you to remember that I'm not Ensign Kim anymore." He snapped, turned and heading off. Seven watched him, then ran after him. She grabbed his arm, causing her to stop and look at her.

"Lieutenant Kim...Harry...I am sorry." She said softly. Harry looked at her, and noticed she was about ready to cry. "I did not mean to...disrespect you or upset you." She said. He sighed, and looked at her.

"I'm sorry, I shouldn't have snapped." Harry said. He looked at her. "Seven, I don't like seeing you upset or hurt. I wanted to help. What happened?" He asked. She looked at him.

"I have been having...problems, dealing with these emotions. Just before we returned from the Delta Quadrant, I had the Doctor remove one of my implants which meant that I would be free to experience human emotions. I did, and I...was hurt." Seven explained. She didn't know why she was opening up, only that it felt right. Harry looked at her, and embraced her in a hug.

"Seven, I know how that feels." He said, as she brought her arms up, allowing the hug to happen. "We've all been there." He added, as they broke apart. "For you, it's new, because you've never felt it before."

"How...how did you handle it?" Seven asked.

"Well, I...I guess that's the hard thing about it. I was pretty torn up. I was in love with Libby, but I found out that she moved on. She's married, has a kid now. But it still hurt because she was my first love." Harry explained. "You never really get over your first love. You always love them, but you move on, in time."

"How? It feels like my heart will never stop hurting." Seven admitted, before explaining how she had gotten involved with Chakotay, and how, and why, it had ended. Harry kept his eyes on her throughout her entire story. He looked at her.

"Seven, I don't think anyone will understand emotions like you do, not even Tuvok. Vulcan's have emotions, they suppress them willingly. You had yours forcibly suppressed. Now you're trying to make up for it and learn about emotions, but at the end of the day, you'll always be behind." Harry said.

"When we first met, you...lusted after me, did you not?" Seven asked. Harry smiled, and nodded.

"Yeah, safe to say I did." Harry confirmed.

"Then perhaps you can assist me." She said, leaning in and kissing him. Harry found himself surprised by the kiss, and wanted to carry it on, but stopped. He pulled back.

"Seven." He said, taking her hands and holding it. "I will say that I would love to help you. But this isn't the best way for me to help." He said. "You're still hurting."

"You do not find me attractive anymore?" Seven asked, feeling hurt. Harry looked at her, his eyes widening.

"Seven, you are very attractive. I like you, a lot. But right now, you're confused. You need to figure out your emotions first. You need to try and decide what you truly want, because I can't be a rebound." Harry said. Seven looked at him.

"I...I understand." She said. He smiled, and embraced her in a hug as the sun began to set behind them.

_Another romance, I know. I hope I've written this well, please give me your feedback, I always welcome it._


	15. Chapter 14 - Something to prove

(San Francisco, Earth)

It was safe to say that Earth was slowly becoming a military base and not the paradise that it was meant to be. Security officers and Marines could be seen on every street of San Francisco, and everyone knew that they were also on the streets in Paris. Construction had already started on a new Federation Council chambers, but in the meantime, the council was meeting at Starfleet Command. Cadet Michael Aravan reflected on how much the planet had changed in the last five months, and not for the better. However, everyone was scared about what might happen, so they were mostly pleased with the increase of security. However, Michael Aravan, a Starfleet Cadet, was using every trick he knew to avoid being seen. He needed to be extremely careful, not only was he out past curfew, he was also planning something very dangerous. Of course, given the current state of affairs, almost everything was dangerous. He was afraid that something bad would happen, so he was being extra careful. As he made his way down an alley, he smiled as he saw the person he was looking for, but stopped when he got a clear view. He had been given a description of the person, but he hadn't expected someone so...young. He shook his head, and approached the kid. "Do you feel safer with the guards?" Michael asked.

"I would feel safer with freedom." The kid replied, completing the code phrase that had been agreed as a precaution.

"So would we all kid." Michael said.

"I'm not a kid." Marcus Schenk said. "I'm old enough to be here."

"Why are you here?" Michael asked, as Marcus handed him a PADD.

"I have my reasons." Marcus replied as Michael read the PADD.

"Like what? I'm here because I'm doing my duty as a Starfleet Officer, protecting the Federation from the idiots that seem to have taken it over." Michael said.

"And I'm dealing with something you wouldn't understand." Marcus said, as he went to walk off. Michael reached out and grabbed his arm.

"I'm sorry." Michael said. "I just want to get an idea of who you are."

"My best friend...he was killed in the Paris bombing. I know the stories, but I don't think Captain Janeway or Captain Picard would have ever done such a thing. I want to find out who killed my friend, and make sure they regret ever doing it." Marcus said. Michael nodded.

"It's not about personal vendetta's kid, but I can understand where you're coming from." Michael said. He looked at the PADD. "We'll stop them, I promise you that." He said.

"Make sure you do." Marcus said, heading off into the darkness. Michael looked at the PADD again and walked off down the path, knowing that the information he held was going to be important to any victory.

As Michael looked around the tunnel he was in, he knew that he was being watched as he walked up to the door of the old bunker from World War 3, which was the base of operations for his cell of the resistance as they were calling themselves. They were using every trick they could to try and find any ship that would be an ally but so far he wasn't having any luck. As he was let into the bunker, he made his way directly to the primary meeting room which had been set up. "Michael, you're late." Captain Alfred Williams said.

"Sorry sir, I've had to be careful with transport." Michael said.

"Did you manage to get the information from the courier?" Commander James Milner asked.

"I did, and quite frankly, it's disturbing. If the information is accurate, and we have no reason to doubt that it is, then we're going to need help as quickly as possible. We need to get word to Voyager somehow, or the Enterprise, or anyone who can help." Michael said.

"I'm not sure I want to hear this." Ambassador Ryan Clarke said. Michael sighed.

"According to our information, the new President of the Federation is also the leader of the Organisation known as Section 31." Michael said.

"Section 31?" Admiral Ross asked, frowning. "I've encountered them before, they wanted to protect the Federation."

"It would seem that their motives have become suspect." Captain S'dan stated.

"Well then, we need to make a plan to get the President out. My guess is that they are using some form of mind control on the Council, no way could they get that many supporters." Michael said.

"So what do you suggest?" Ross asked.

"How about we launch an attack on the President. We could take in a strike team, and take him out." Ensign Drake suggested.

"We wouldn't get through the front door." Ross said, shaking his head. "No, we need a diversion."

"Then we need to find a ship to find Voyager. They were the ones leading this, if our reports are accurate." Captain Williams stated.

"I'll go. I can get on a transport, and find a ship to help me search." Michael said. Everyone looked at him.

"No offence Cadet, but you're not ready for this." Ross said. Michael looked at them.

"Admiral, I took an oath to defend the Federation and to do my duty. If my duty requires me to locate Voyager and our allies, then so be it." Michael said. "I have skills in security. I am a part of Red Squad, and I trust my squad. Let us do it. We can do it."

"It would be easy to assign Red Squad to a ship as a training exercise." Captain S'dan said.

"In fact, the USS Valiant A is ready for launch, and she has a cloaking device." Admiral Necheyev stated. Ross nodded.

"Very well. You leave in the morning. Good luck Cadet." Ross said.

(Two days later)

Michael sighed as he looked at the viewscreen. "Are you sure?" He asked.

"Positive." Cadet Lewis Martin replied from the Operations station. "No sign of anyone."

"Will, take us to the next sector." Michael said. The helm officer, Cadet William Alvarez nodded and set in the course.

"Can I suggest something?" Cadet Andrew Roach asked. Michael nodded.

"Anything Andy." Michael replied.

"We need to think more like rebels. I say we head to the badlands. After all, Commander Chakotay used to be in the Maquis, and that used to be a base for them, didn't it?" Andy asked. Michael nodded, and stood up.

"Will, you heard the man." Michael said. As the Valiant went to warp, Michael felt a darkness inside of him, something he was dreading. He had been given a mission, and now here he was, facing one of the darkest enemies, and he was, for all intents and purposes, at war. He had lived to see the Dominion War, the attacks by the Borg, the Cardassians, the Maquis and now the Federation itself. It reminded him of something he had heard before, a saying he had read back at school...

"_Only the dead have seen the end of war._"

_Hey guys, sorry this took so long, things have been hectic recently. I hope you like this chapter. As I always address issues and points raised, QOP raised a few points. 1) At this state, Janeway is just a Captain, not an Admiral, I'll reach that point sometime. 2) Yes, they know of the Enterprise and such but they can't risk leaving their hiding place to search for the Enterprise and co. Their story will be told later. And as for the pairings, I always write how I think the characters would react, especially since I have met Kate Mulgrew who has said she would have liked to have seen Chakotay and Janeway together, but nothing would have gotten done. Still, I think their story needs to be told. However, I can always write another story later if you have a specific pairing, but it would need to flow naturally because I would not want to make the characters non canonical if you know what I mean? But there could be some romance there._


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